protocols::frag_picker::BoundedCollector< StrictWeakOrdering > Class Template Reference

Keeps the N best fragments candidates for the final selection. More...

#include <BoundedCollector.hh>

Public Types
typedef utility::pointer::owning_ptr < BoundedCollector < StrictWeakOrdering > >	BoundedCollectorOP
typedef utility::pointer::owning_ptr < BoundedCollector < StrictWeakOrdering > const >	BoundedCollectorCOP

Public Member Functions
	BoundedCollector (Size query_size, Size max_frags_per_pos, StrictWeakOrdering fragment_comparator, Size n_score_terms, Size buffer_factor=5)
	create a collector for a given size of a query sequence More...
bool	add (ScoredCandidate new_canditate)
	Insert a fragment candidate to the container. More...
Size	count_candidates (Size seq_pos) const
	Check how many candidates have been already collected for a given position APL Note: you cannot have inlined virtual functions. More...
Size	count_candidates () const
	Check how many candidates have been already collected for all positions APL Note: you cannot have inlined virtual functions. More...
Size	query_length () const
	Check the size of query sequence that this object knows. This is mainly to be able to check if it is the same as in the other parts of fragment picking machinery. More...
void	insert (Size pos, CandidatesCollectorOP collector)
	Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate. More...
ScoredCandidatesVector1 &	get_candidates (Size position_in_query)
	returns all stored fragment candidates that begins at a given position in a query More...
void	clear ()
	removes all candidates from the container More...
void	print_report (std::ostream &out, scores::FragmentScoreManagerOP scoring) const
	prints how many candidates have been collected for each position and how good they are More...

Private Attributes
utility::vector1 < LazySortedVector1< std::pair < FragmentCandidateOP, scores::FragmentScoreMapOP > , StrictWeakOrdering > >	storage_

Detailed Description

template<class StrictWeakOrdering>
class protocols::frag_picker::BoundedCollector< StrictWeakOrdering >

Keeps the N best fragments candidates for the final selection.

Detailed: The purpose of a collector is to keep the best fragment candidates to the end

of vall processing. In particular, the capacity of this collector may be larger than the number of fragments one wants to get

Member Typedef Documentation

template<class StrictWeakOrdering>

typedef utility::pointer::owning_ptr< BoundedCollector< StrictWeakOrdering > const> protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollectorCOP

template<class StrictWeakOrdering>

typedef utility::pointer::owning_ptr< BoundedCollector< StrictWeakOrdering > > protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollectorOP

Constructor & Destructor Documentation

template<class StrictWeakOrdering>

protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::BoundedCollector ( Size  query_size, Size  max_frags_per_pos, StrictWeakOrdering  fragment_comparator, Size  n_score_terms, Size  buffer_factor = 5  )

inline

create a collector for a given size of a query sequence

Member Function Documentation

template<class StrictWeakOrdering>

bool protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::add ( ScoredCandidate  new_canditate )

inlinevirtual

Insert a fragment candidate to the container.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>

void protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::clear ( )

inlinevirtual

removes all candidates from the container

Implements protocols::frag_picker::CandidatesCollector.

Referenced by protocols::frag_picker::BoundedCollector< CompareTotalScore >::clear().

template<class StrictWeakOrdering>

Size protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::count_candidates ( Size  seq_pos ) const

inlinevirtual

Check how many candidates have been already collected for a given position APL Note: you cannot have inlined virtual functions.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>

Size protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::count_candidates ( ) const

inlinevirtual

Check how many candidates have been already collected for all positions APL Note: you cannot have inlined virtual functions.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>

ScoredCandidatesVector1& protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::get_candidates ( Size  position_in_query )

inlinevirtual

returns all stored fragment candidates that begins at a given position in a query

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>

void protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::insert ( Size  pos, CandidatesCollectorOP  collector  )

inlinevirtual

Inserts candidates from another Collector for a give position in the query Candidates may or may not get inserted depending on the candidate.

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>

void protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::print_report ( std::ostream &  out, scores::FragmentScoreManagerOP  scoring  ) const

inlinevirtual

prints how many candidates have been collected for each position and how good they are

Implements protocols::frag_picker::CandidatesCollector.

template<class StrictWeakOrdering>

Size protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::query_length ( ) const

inlinevirtual

Check the size of query sequence that this object knows. This is mainly to be able to check if it is the same as in the other parts of fragment picking machinery.

Implements protocols::frag_picker::CandidatesCollector.

Member Data Documentation

template<class StrictWeakOrdering>

utility::vector1< LazySortedVector1< std::pair< FragmentCandidateOP, scores::FragmentScoreMapOP> , StrictWeakOrdering> > protocols::frag_picker::BoundedCollector< StrictWeakOrdering >::storage_

private

Referenced by protocols::frag_picker::BoundedCollector< CompareTotalScore >::add(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::BoundedCollector(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::clear(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::count_candidates(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::get_candidates(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::insert(), protocols::frag_picker::BoundedCollector< CompareTotalScore >::print_report(), and protocols::frag_picker::BoundedCollector< CompareTotalScore >::query_length().

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The documentation for this class was generated from the following files:

• src/protocols/frag_picker/BoundedCollector.fwd.hh
• src/protocols/frag_picker/BoundedCollector.hh